DescriptionThe theoretical method of choice for studies of cellular processes is molecular dynamics. In molecular dynamics Newtonian equations of motion are solved with bonds, angles and dihedrals described with various force constants. While simple, this simple approach forms the basis of our understanding of processes as diverse as lipid raft formation and the molecular mechanism of the recognition between enzyme and its substrate. When constructing such systems great care must be taken to make it as realistic as possible, which means accounting for the local environment such as water or cellular membrane, physiological conditions, … this may in turn may make the system large enough to warrant running the simulations on supercomputers. While not long the choice was rather simple – number of CPUs, it has in recent years with the advent of specialized accelerators such as Nvidia’s CUDA and Intel Phi become much less straightforward. In this work we evaluated the performance of supercomputers based on x86_64, Intel Phi and Sunway architectures for simulations of several large biosystems. Our results show that in order to really harness the power of these emerging technologies it is necessary to optimize many of the production codes used today, which is not trivial.